For information on updates to the publicly available 10x Genomics transcriptome and V(D)J references, please refer to the reference release notes.
10x Genomics offers pre-built Cell Ranger reference packages from the downloads page. For purposes of reproducibility, the exact build steps are provided here.
# Genome metadata
genome="GRCh38"
version="2024-A"
# Set up source and build directories
build="GRCh38-GENCODEv44_build"
mkdir -p "$build"
# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"
# Using release 109 FASTA for GRCh38 instead of release 110 FASTA -- release 110 moved from GRCh38.p13 to GRCh38.p14,
# which unmasked the pseudo-autosomal region. This causes ambiguous mappings to PAR locus genes.
# No other sequence changes were made to the primary assembly.
fasta_url="http://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
fasta_in="${source}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.primary_assembly.annotation.gtf.gz"
gtf_in="${source}/gencode.v44.primary_assembly.annotation.gtf"
if [ ! -f "$fasta_in" ]; then
curl -sS "$fasta_url" | zcat > "$fasta_in"
fi
if [ ! -f "$gtf_in" ]; then
curl -sS "$gtf_url" | zcat > "$gtf_in"
fi
# Modify sequence headers in the Ensembl FASTA to match the file
# "GRCh38.primary_assembly.genome.fa" from GENCODE. Unplaced and unlocalized
# sequences such as "KI270728.1" have the same names in both versions.
#
# Input FASTA:
# >1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF
#
# Output FASTA:
# >chr1 1
fasta_modified="$build/$(basename "$fasta_in").modified"
# sed commands:
# 1. Replace metadata after space with original contig name, as in GENCODE
# 2. Add "chr" to names of autosomes and sex chromosomes
# 3. Handle the mitochrondrial chromosome
cat "$fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$fasta_modified"
# Remove version suffix from transcript, gene, and exon IDs in order to match
# previous Cell Ranger reference packages
#
# Input GTF:
# ... gene_id "ENSG00000223972.5"; ...
# Output GTF:
# ... gene_id "ENSG00000223972"; gene_version "5"; ...
gtf_modified="$build/$(basename "$gtf_in").modified"
# Pattern matches Ensembl gene, transcript, and exon IDs for human or mouse:
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
cat "$gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$gtf_modified"
# Define string patterns for GTF tags
# NOTES:
# Since Ensembl 110, polymorphic pseudogenes are now just protein_coding.
# Readthrough genes are annotated with the readthrough_transcript tag.
BIOTYPE_PATTERN=\
"(protein_coding|protein_coding_LoF|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
# Construct the gene ID allowlist. We filter the list of all transcripts
# based on these criteria:
# - allowable gene_type (biotype)
# - allowable transcript_type (biotype)
# - no "readthrough_transcript" tag
# We then collect the list of gene IDs that have at least one associated
# transcript passing the filters.
cat "$gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
# NOTES:
# Since Ensembl 110, the PAR locus genes are included on chrY as copies of chrX
# Using the GRCh38.p13 assembly hard masks these regions on chrY, but removing the
# chrY PAR genes is still desirable so they do not end up as extra entries in the output.
# The awk command below excludes all PAR_Y genes, including XGY2.
# The non-coding gene XGY2 straddles the PAR1 boundary on chrY, and is homologous to XG on chrX.
# GRCh38-2024-A excludes XGY2, but includes SRY and ENSG00000286130, which are in an intron of XGY2,
# and RPS4Y1, which overlaps XGY2.
# Filter the GTF file based on the gene allowlist
gtf_filtered="${build}/$(basename "$gtf_in").filtered"
# Copy header lines beginning with "#"
grep -E "^#" "$gtf_modified" > "$gtf_filtered"
# Filter to the gene allowlist, and then remove PAR_Y genes
grep -Ff "${build}/gene_allowlist" "$gtf_modified" \
| awk -F "\t" '$1 != "chrY" || $1 == "chrY" && $4 >= 2752083 && $4 < 56887903 && !/ENSG00000290840/' \
>> "$gtf_filtered"
# Create reference package
cellranger mkref --ref-version="$version" \
--genome="$genome" --fasta="$fasta_modified" --genes="$gtf_filtered" \
--nthreads=16
# Genome metadata
genome="GRCm39"
version="2024-A"
# Set up source and build directories
build="GRCm39-GENCODEv33_build"
mkdir -p "$build"
# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"
fasta_url="http://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz"
fasta_in="${source}/Mus_musculus.GRCm39.dna.primary_assembly.fa"
gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M33/gencode.vM33.primary_assembly.annotation.gtf.gz"
gtf_in="${source}/gencode.vM33.primary_assembly.annotation.gtf"
if [ ! -f "$fasta_in" ]; then
curl -sS "$fasta_url" | zcat > "$fasta_in"
fi
if [ ! -f "$gtf_in" ]; then
curl -sS "$gtf_url" | zcat > "$gtf_in"
fi
# Modify sequence headers in the Ensembl FASTA to match the file
# "GRCm38.primary_assembly.genome.fa" from GENCODE. Unplaced and unlocalized
# sequences such as "GL456210.1" have the same names in both versions.
#
# Input FASTA:
# >1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF
#
# Output FASTA:
# >chr1 1
fasta_modified="$build/$(basename "$fasta_in").modified"
# sed commands:
# 1. Replace metadata after space with original contig name, as in GENCODE
# 2. Add "chr" to names of autosomes and sex chromosomes
# 3. Handle the mitochrondrial chromosome
cat "$fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$fasta_modified"
# Remove version suffix from transcript, gene, and exon IDs in order to match
# previous Cell Ranger reference packages
#
# Input GTF:
# ... gene_id "ENSMUSG00000102693.1"; ...
# Output GTF:
# ... gene_id "ENSMUSG00000102693"; gene_version "1"; ...
gtf_modified="$build/$(basename "$gtf_in").modified"
# Pattern matches Ensembl gene, transcript, and exon IDs for human or mouse:
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
cat "$gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$gtf_modified"
# Define string patterns for GTF tags
# Since Ensembl 110, polymorphic pseudogenes are now just protein_coding.
# Readthrough genes are annotated with the readthrough_transcript tag.
BIOTYPE_PATTERN=\
"(protein_coding|protein_coding_LoF|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
# Construct the gene ID allowlist. We filter the list of all transcripts
# based on these criteria:
# - allowable gene_type (biotype)
# - allowable transcript_type (biotype)
# - no "readthrough_transcript" tag
# We then collect the list of gene IDs that have at least one associated
# transcript passing the filters.
cat "$gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
# Filter the GTF file based on the gene allowlist
gtf_filtered="${build}/$(basename "$gtf_in").filtered"
# Copy header lines beginning with "#"
grep -E "^#" "$gtf_modified" > "$gtf_filtered"
# Filter to the gene allowlist
grep -Ff "${build}/gene_allowlist" "$gtf_modified" \
>> "$gtf_filtered"
# Create reference package
cellranger mkref --ref-version="$version" \
--genome="$genome" --fasta="$fasta_modified" --genes="$gtf_filtered" \
--nthreads=16
#################### SETUP ####################
human_genome="GRCh38"
mouse_genome="GRCm39"
version="2024-A"
build="GRCh38_and_GRCm39_GENCODEv44-GENCODEvm33"
mkdir -p "$build"
# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"
# Using release 109 for GRCh38 instead of release 110 -- release 110 moved from GRCh38.p13 to GRCh38.p14,
# which unmasked the pseudo-autosomal region. This causes ambiguous mappings to PAR locus genes.
human_fasta_url="http://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
human_fasta_in="${source}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
human_gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.primary_assembly.annotation.gtf.gz"
human_gtf_in="${source}/gencode.v44.primary_assembly.annotation.gtf"
mouse_fasta_url="http://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz"
mouse_fasta_in="${source}/Mus_musculus.GRCm39.dna.primary_assembly.fa"
mouse_gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M33/gencode.vM33.primary_assembly.annotation.gtf.gz"
mouse_gtf_in="${source}/gencode.vM33.primary_assembly.annotation.gtf"
if [ ! -f "$human_fasta_in" ]; then
curl -sS "$human_fasta_url" | zcat > "$human_fasta_in"
fi
if [ ! -f "$human_gtf_in" ]; then
curl -sS "$human_gtf_url" | zcat > "$human_gtf_in"
fi
if [ ! -f "$mouse_fasta_in" ]; then
curl -sS "$mouse_fasta_url" | zcat > "$mouse_fasta_in"
fi
if [ ! -f "$mouse_gtf_in" ]; then
curl -sS "$mouse_gtf_url" | zcat > "$mouse_gtf_in"
fi
# String patterns used for both genomes
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
BIOTYPE_PATTERN=\
"(protein_coding|protein_coding_LoF|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
# Process FASTA -- translate chromosome names
human_fasta_modified="$build/$(basename "$human_fasta_in").modified"
cat "$human_fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$human_fasta_modified"
# Process GTF -- split Ensembl IDs from version suffixes
human_gtf_modified="$build/$(basename "$human_gtf_in").modified"
cat "$human_gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$human_gtf_modified"
# Process GTF -- filter based on gene/transcript tags
cat "$human_gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
human_gtf_filtered="${build}/$(basename "$human_gtf_in").filtered"
grep -E "^#" "$human_gtf_modified" > "$human_gtf_filtered"
grep -Ff "${build}/gene_allowlist" "$human_gtf_modified" \
| awk -F "\t" '$1 != "chrY" || $1 == "chrY" && $4 >= 2752083 && $4 < 56887903 && !/ENSG00000290840/' \
>> "$human_gtf_filtered"
#################### MOUSE ####################
# Please see the GRCm39-2024-A build documentation for details on these steps.
# Process FASTA -- translate chromosome names
mouse_fasta_modified="$build/$(basename "$mouse_fasta_in").modified"
cat "$mouse_fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$mouse_fasta_modified"
# Process GTF -- split Ensembl IDs from version suffixes
mouse_gtf_modified="$build/$(basename "$mouse_gtf_in").modified"
cat "$mouse_gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$mouse_gtf_modified"
# Process GTF -- filter based on gene/transcript tags
cat "$mouse_gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
mouse_gtf_filtered="${build}/$(basename "$mouse_gtf_in").filtered"
grep -E "^#" "$mouse_gtf_modified" > "$mouse_gtf_filtered"
grep -Ff "${build}/gene_allowlist" "$mouse_gtf_modified" \
>> "$mouse_gtf_filtered"
#################### MKREF ####################
cellranger mkref --ref-version="$version" \
--genome="$human_genome" --fasta="$human_fasta_modified" --genes="$human_gtf_filtered" \
--genome="$mouse_genome" --fasta="$mouse_fasta_modified" --genes="$mouse_gtf_filtered" \
--nthreads=16
# Genome metadata
genome="GRCh38"
version="2020-A"
# Set up source and build directories
build="GRCh38-2020-A_build"
mkdir -p "$build"
# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"
fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
fasta_in="${source}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.primary_assembly.annotation.gtf.gz"
gtf_in="${source}/gencode.v32.primary_assembly.annotation.gtf"
if [ ! -f "$fasta_in" ]; then
curl -sS "$fasta_url" | zcat > "$fasta_in"
fi
if [ ! -f "$gtf_in" ]; then
curl -sS "$gtf_url" | zcat > "$gtf_in"
fi
# Modify sequence headers in the Ensembl FASTA to match the file
# "GRCh38.primary_assembly.genome.fa" from GENCODE. Unplaced and unlocalized
# sequences such as "KI270728.1" have the same names in both versions.
# Input FASTA:
# >1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF
# Output FASTA:
# >chr1 1
fasta_modified="$build/$(basename "$fasta_in").modified"
# sed commands:
# 1. Replace metadata after space with original contig name, as in GENCODE
# 2. Add "chr" to names of autosomes and sex chromosomes
# 3. Handle the mitochondrial chromosome
cat "$fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$fasta_modified"
# Remove version suffix from transcript, gene, and exon IDs in order to match
# previous Cell Ranger reference packages
# Input GTF:
# ... gene_id "ENSG00000223972.5"; ...
# Output GTF:
# ... gene_id "ENSG00000223972"; gene_version "5"; ...
gtf_modified="$build/$(basename "$gtf_in").modified"
# Pattern matches Ensembl gene, transcript, and exon IDs for human or mouse:
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
cat "$gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$gtf_modified"
# Define string patterns for GTF tags
# NOTES:
# - Since GENCODE release 31/M22 (Ensembl 97), the "lincRNA" and "antisense"
# biotypes are part of a more generic "lncRNA" biotype.
# - These filters are relevant only to GTF files from GENCODE. The GTFs from
# Ensembl release 98 have the following differences:
# - The names "gene_biotype" and "transcript_biotype" are used instead of
# "gene_type" and "transcript_type".
# - Readthrough transcripts are present but are not marked with the
# "readthrough_transcript" tag.
# - Only the X chromosome versions of genes in the pseudoautosomal regions
# are present, so there is no "PAR" tag.
BIOTYPE_PATTERN=\
"(protein_coding|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
PAR_PATTERN="tag \"PAR\""
# Construct the gene ID allowlist. We filter the list of all transcripts
# based on these criteria:
# - allowable gene_type (biotype)
# - allowable transcript_type (biotype)
# - no "PAR" tag (only present for Y chromosome PAR)
# - no "readthrough_transcript" tag
# We then collect the list of gene IDs that have at least one associated
# transcript passing the filters.
cat "$gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| grep -Ev "$PAR_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
# Filter the GTF file based on the gene allowlist
gtf_filtered="${build}/$(basename "$gtf_in").filtered"
# Copy header lines beginning with "#"
grep -E "^#" "$gtf_modified" > "$gtf_filtered"
# Filter to the gene allowlist
grep -Ff "${build}/gene_allowlist" "$gtf_modified" \
>> "$gtf_filtered"
# Create reference package
cellranger mkref --ref-version="$version" \
--genome="$genome" --fasta="$fasta_modified" --genes="$gtf_filtered"
# Genome metadata
genome="mm10"
version="2020-A"
# Set up source and build directories
build="mm10-2020-A_build"
mkdir -p "$build"
# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"
fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz"
fasta_in="${source}/Mus_musculus.GRCm38.dna.primary_assembly.fa"
gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz"
gtf_in="${source}/gencode.vM23.primary_assembly.annotation.gtf"
if [ ! -f "$fasta_in" ]; then
curl -sS "$fasta_url" | zcat > "$fasta_in"
fi
if [ ! -f "$gtf_in" ]; then
curl -sS "$gtf_url" | zcat > "$gtf_in"
fi
# Modify sequence headers in the Ensembl FASTA to match the file
# "GRCm38.primary_assembly.genome.fa" from GENCODE. Unplaced and unlocalized
# sequences such as "GL456210.1" have the same names in both versions.
# Input FASTA:
# >1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF
# Output FASTA:
# >chr1 1
fasta_modified="$build/$(basename "$fasta_in").modified"
# sed commands:
# 1. Replace metadata after space with original contig name, as in GENCODE
# 2. Add "chr" to names of autosomes and sex chromosomes
# 3. Handle the mitochrondrial chromosome
cat "$fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$fasta_modified"
# Remove version suffix from transcript, gene, and exon IDs in order to match
# previous Cell Ranger reference packages
# Input GTF:
# ... gene_id "ENSMUSG00000102693.1"; ...
# Output GTF:
# ... gene_id "ENSMUSG00000102693"; gene_version "1"; ...
gtf_modified="$build/$(basename "$gtf_in").modified"
# Pattern matches Ensembl gene, transcript, and exon IDs for human or mouse:
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
cat "$gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$gtf_modified"
# Define string patterns for GTF tags
# NOTES:
# - Since GENCODE release 31/M22 (Ensembl 97), the "lincRNA" and "antisense"
# biotypes are part of a more generic "lncRNA" biotype.
# - These filters are relevant only to GTF files from GENCODE. The GTFs from
# Ensembl release 98 have the following differences:
# - The names "gene_biotype" and "transcript_biotype" are used instead of
# "gene_type" and "transcript_type".
# - Readthrough transcripts are present but are not marked with the
# "readthrough_transcript" tag.
BIOTYPE_PATTERN=\
"(protein_coding|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
# Construct the gene ID allowlist. We filter the list of all transcripts
# based on these criteria:
# - allowable gene_type (biotype)
# - allowable transcript_type (biotype)
# - no "readthrough_transcript" tag
# We then collect the list of gene IDs that have at least one associated
# transcript passing the filters.
cat "$gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
# Filter the GTF file based on the gene allowlist
gtf_filtered="${build}/$(basename "$gtf_in").filtered"
# Copy header lines beginning with "#"
grep -E "^#" "$gtf_modified" > "$gtf_filtered"
# Filter to the gene allowlist
grep -Ff "${build}/gene_allowlist" "$gtf_modified" \
>> "$gtf_filtered"
# Create reference package
cellranger mkref --ref-version="$version" \
--genome="$genome" --fasta="$fasta_modified" --genes="$gtf_filtered"
#################### SETUP ####################
human_genome="GRCh38"
mouse_genome="mm10"
version="2020-A"
build="GRCh38_and_mm10-2020-A_build"
mkdir -p "$build"
# Download source files if they do not exist in reference_sources/ folder
source="reference_sources"
mkdir -p "$source"
human_fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
human_fasta_in="${source}/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
human_gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.primary_assembly.annotation.gtf.gz"
human_gtf_in="${source}/gencode.v32.primary_assembly.annotation.gtf"
mouse_fasta_url="http://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz"
mouse_fasta_in="${source}/Mus_musculus.GRCm38.dna.primary_assembly.fa"
mouse_gtf_url="http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz"
mouse_gtf_in="${source}/gencode.vM23.primary_assembly.annotation.gtf"
if [ ! -f "$human_fasta_in" ]; then
curl -sS "$human_fasta_url" | zcat > "$human_fasta_in"
fi
if [ ! -f "$human_gtf_in" ]; then
curl -sS "$human_gtf_url" | zcat > "$human_gtf_in"
fi
if [ ! -f "$mouse_fasta_in" ]; then
curl -sS "$mouse_fasta_url" | zcat > "$mouse_fasta_in"
fi
if [ ! -f "$mouse_gtf_in" ]; then
curl -sS "$mouse_gtf_url" | zcat > "$mouse_gtf_in"
fi
# String patterns used for both genomes
ID="(ENS(MUS)?[GTE][0-9]+)\.([0-9]+)"
BIOTYPE_PATTERN=\
"(protein_coding|lncRNA|\
IG_C_gene|IG_D_gene|IG_J_gene|IG_LV_gene|IG_V_gene|\
IG_V_pseudogene|IG_J_pseudogene|IG_C_pseudogene|\
TR_C_gene|TR_D_gene|TR_J_gene|TR_V_gene|\
TR_V_pseudogene|TR_J_pseudogene)"
GENE_PATTERN="gene_type \"${BIOTYPE_PATTERN}\""
TX_PATTERN="transcript_type \"${BIOTYPE_PATTERN}\""
READTHROUGH_PATTERN="tag \"readthrough_transcript\""
PAR_PATTERN="tag \"PAR\""
#################### HUMAN ####################
# Please see the GRCh38-2020-A build documentation for details on these steps.
# Process FASTA -- translate chromosome names
human_fasta_modified="$build/$(basename "$human_fasta_in").modified"
cat "$human_fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$human_fasta_modified"
# Process GTF -- split Ensembl IDs from version suffixes
human_gtf_modified="$build/$(basename "$human_gtf_in").modified"
cat "$human_gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$human_gtf_modified"
# Process GTF -- filter based on gene/transcript tags
cat "$human_gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| grep -Ev "$PAR_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
human_gtf_filtered="${build}/$(basename "$human_gtf_in").filtered"
grep -E "^#" "$human_gtf_modified" > "$human_gtf_filtered"
grep -Ff "${build}/gene_allowlist" "$human_gtf_modified" \
>> "$human_gtf_filtered"
#################### MOUSE ####################
# Please see the mm10-2020-A build documentation for details on these steps.
# Process FASTA -- translate chromosome names
mouse_fasta_modified="$build/$(basename "$mouse_fasta_in").modified"
cat "$mouse_fasta_in" \
| sed -E 's/^>(\S+).*/>\1 \1/' \
| sed -E 's/^>([0-9]+|[XY]) />chr\1 /' \
| sed -E 's/^>MT />chrM /' \
> "$mouse_fasta_modified"
# Process GTF -- split Ensembl IDs from version suffixes
mouse_gtf_modified="$build/$(basename "$mouse_gtf_in").modified"
cat "$mouse_gtf_in" \
| sed -E 's/gene_id "'"$ID"'";/gene_id "\1"; gene_version "\3";/' \
| sed -E 's/transcript_id "'"$ID"'";/transcript_id "\1"; transcript_version "\3";/' \
| sed -E 's/exon_id "'"$ID"'";/exon_id "\1"; exon_version "\3";/' \
> "$mouse_gtf_modified"
# Process GTF -- filter based on gene/transcript tags
cat "$mouse_gtf_modified" \
| awk '$3 == "transcript"' \
| grep -E "$GENE_PATTERN" \
| grep -E "$TX_PATTERN" \
| grep -Ev "$READTHROUGH_PATTERN" \
| sed -E 's/.*(gene_id "[^"]+").*/\1/' \
| sort \
| uniq \
> "${build}/gene_allowlist"
mouse_gtf_filtered="${build}/$(basename "$mouse_gtf_in").filtered"
grep -E "^#" "$mouse_gtf_modified" > "$mouse_gtf_filtered"
grep -Ff "${build}/gene_allowlist" "$mouse_gtf_modified" \
>> "$mouse_gtf_filtered"
#################### MKREF ####################
cellranger mkref --ref-version="$version" \
--genome="$human_genome" --fasta="$human_fasta_modified" --genes="$human_gtf_filtered" \
--genome="$mouse_genome" --fasta="$mouse_fasta_modified" --genes="$mouse_gtf_filtered"
wget ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz
gunzip Homo_sapiens.GRCh38.93.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz
gunzip Mus_musculus.GRCm38.93.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh38.93.gtf Homo_sapiens.GRCh38.93.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkgtf Mus_musculus.GRCm38.93.gtf Mus_musculus.GRCm38.93.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkref --genome=GRCh38 \
--fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh38.93.filtered.gtf \
--genome=mm10 \
--fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
--genes=Mus_musculus.GRCm38.93.filtered.gtf \
--ref-version=3.1.0
wget ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz
gunzip Homo_sapiens.GRCh38.93.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh38.93.gtf Homo_sapiens.GRCh38.93.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkref --genome=GRCh38 \
--fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh38.93.filtered.gtf \
--ref-version=3.0.0
wget ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
gunzip Homo_sapiens.GRCh37.87.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.87.gtf Homo_sapiens.GRCh37.87.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense
cellranger mkref --genome=hg19 \
--fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh37.87.filtered.gtf \
--ref-version=3.0.0
wget ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz
gunzip Mus_musculus.GRCm38.93.gtf.gz
cellranger mkgtf Mus_musculus.GRCm38.93.gtf Mus_musculus.GRCm38.93.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkref --genome=mm10 \
--fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
--genes=Mus_musculus.GRCm38.93.filtered.gtf \
--ref-version=3.0.0
wget ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
gunzip Homo_sapiens.GRCh37.87.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-93/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.gtf.gz
gunzip Mus_musculus.GRCm38.93.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.87.gtf Homo_sapiens.GRCh37.87.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkgtf Mus_musculus.GRCm38.93.gtf Mus_musculus.GRCm38.93.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkref --genome=hg19 \
--fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh37.87.filtered.gtf \
--genome=mm10 \
--fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
--genes=Mus_musculus.GRCm38.93.filtered.gtf \
--ref-version=3.0.0
wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz
gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkref --genome=mm10 \
--fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
--genes=Mus_musculus.GRCm38.84.filtered.gtf \
--ref-version=2.1.0
wget ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz
gunzip Homo_sapiens.GRCh37.82.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz
gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.82.gtf Homo_sapiens.GRCh37.82.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkref --genome=hg19 \
--fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh37.82.filtered.gtf \
--genome=mm10 \
--fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
--genes=Mus_musculus.GRCm38.84.filtered.gtf \
--ref-version=2.1.0
wget ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz
gunzip Homo_sapiens.GRCh38.84.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh38.84.gtf Homo_sapiens.GRCh38.84.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--attribute=gene_biotype:IG_V_pseudogene \
--attribute=gene_biotype:IG_D_gene \
--attribute=gene_biotype:IG_J_gene \
--attribute=gene_biotype:IG_J_pseudogene \
--attribute=gene_biotype:IG_C_gene \
--attribute=gene_biotype:IG_C_pseudogene \
--attribute=gene_biotype:TR_V_gene \
--attribute=gene_biotype:TR_V_pseudogene \
--attribute=gene_biotype:TR_D_gene \
--attribute=gene_biotype:TR_J_gene \
--attribute=gene_biotype:TR_J_pseudogene \
--attribute=gene_biotype:TR_C_gene
cellranger mkref --genome=GRCh38 \
--fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh38.84.filtered.gtf \
--ref-version=1.2.0
wget ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz
gunzip Homo_sapiens.GRCh37.82.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.82.gtf Homo_sapiens.GRCh37.82.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense
cellranger mkref --genome=hg19 \
--fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh37.82.filtered.gtf \
--ref-version=1.2.0
wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz
gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense
cellranger mkref --genome=mm10 \
--fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
--genes=Mus_musculus.GRCm38.84.filtered.gtf \
--ref-version=1.2.0
wget ftp://ftp.ensembl.org/pub/grch37/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
gunzip Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/grch37/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh37.82.gtf.gz
gunzip Homo_sapiens.GRCh37.82.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-84/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
wget ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz
gunzip Mus_musculus.GRCm38.84.gtf.gz
cellranger mkgtf Homo_sapiens.GRCh37.82.gtf Homo_sapiens.GRCh37.82.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense
cellranger mkref --genome=hg19 \
--fasta=Homo_sapiens.GRCh37.dna.primary_assembly.fa \
--genes=Homo_sapiens.GRCh37.82.filtered.gtf \
--genome=mm10 \
--fasta=Mus_musculus.GRCm38.dna.primary_assembly.fa \
--genes=Mus_musculus.GRCm38.84
cellranger mkref --genome=ercc92 \
--fasta=ercc92.fa \
--genes=ercc92.gtf \
--ref-version=1.2.0